prokka跑fasta数据时，为什么出现了这些问题

[dedeqq11111]

Running: prodigal -i PROKKA_04122024/PROKKA_04122024.fna -c -m -g 11 -p single -f sco -q [19:56:37] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + strand [19:56:39] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:1287065..1287631 on + strand [19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2727331..2727450 on - strand [19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2729716..2729970 on - strand [19:56:41] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:2817923..2818393 on + strand [19:56:42] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:3423503..3423826 on + strand [19:56:42] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3427321..3427575 on - strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3942995..3943249 on + strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4036718..4036972 on + strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4167846..4168100 on + strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4170375..4170494 on + strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4209334..4209588 on + strand [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4211777..4211896 on + strand [19:56:43] Found 4305 CDS [19:56:43] Connecting features back to sequences [19:56:43] Not using genus-specific database. Try --usegenus to enable it. [19:56:43] Annotating CDS, please be patient. [19:56:43] Will use 8 CPUs for similarity searching. [19:56:44] There are still 4305 unannotated CDS left (started with 4305) [19:56:44] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/IS with 8 CPUs [19:56:44] Running: cat PROKKA_04122024/IS.faa | parallel --gnu --plain -j 8 --block 86286 --recstart '>' --pipe blastp -query - -db /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_04122024/IS.blast 2> /dev/null [19:56:57] Deleting unwanted file: PROKKA_04122024/IS.faa [19:56:57] Deleting unwanted file: PROKKA_04122024/IS.blast [19:56:58] There are still 4229 unannotated CDS left (started with 4305) [19:56:58] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/AMR with 8 CPUs [19:56:58] Running: cat PROKKA_04122024/AMR.faa | parallel --gnu --plain -j 8 --block 85153 --recstart '>' --pipe blastp -query - -db /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_04122024/AMR.blast 2> /dev/null [19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.faa [19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.blast [19:57:09] There are still 4229 unannotated CDS left (started with 4305) [19:57:09] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/sprot with 8 CPUs [19:57:09] Running: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --recstart '>' --pipe blastp -query - -db /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_04122024/sprot.blast 2> /dev/null [19:57:52] Could not run command: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --recstart '>' --pipe blastp -query - -db /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_04122024/sprot.blast 2> /dev/null

[shenwei356]

Title translation:

Why do these problems occur when running these fasta data with prokka?